The directory $toaderDir.'/autodoc/' under a Toader directory is used for storing AutoDoc settings for that Toader directory.

The file $toaderDir.'/autodoc/dirs' is to store the paths under the that Toader that should be searched for documentation.
The paths in the file is are relative to the Toader directory in question and may not match any of the of the regular expressions below.

^\.\.
\.\.$
\/\.\.\/

Files are considered to be documentation if they match any of the regular expressions below.

Once that is written out, the files are copied to $outputDir.'/'.$r2r.'/.autodoc/.files/', with the page used the relative path of copied documentation in regards to the Toader directory in question. POD files and Perl modules are passed through a POD to HTML converter and have '.html' appended to the file name.